P02-01
Investigation of the Allosteric Binding Sites of ERK2 by Metadynamics Simulation
Hajime SUGIYAMA *1, Seisuke HASEGAWA2, Mayu YOSHIDA2, Takayoshi KINOSHITA2
1Mitsubishi Chemical Corp.
2Osaka Metropolitan University
( * E-mail: hajime.sugiyama.ma@mcgc.com )
ERK2 (extracellular signal-regulated kinase 2) is a member of the mitogen-activated protein kinase family. STAT3 (signal transducer and activator of transcription 3), which plays an essential role in normal glucose homeostasis, and regulates cell proliferation, differentiation, and various other cellular responses. Based on previous studies on the ERK2/STAT3 pathway, the authors focused on ERK2 as a candidate target for diabetes treatment and identified small molecule compounds with inhibitory activity through in silico screening[1].
The crystal structures of ERK2 in complex with the compounds revealed that one previously reported inhibitor binds to a novel allosteric site in close proximity to the TXY motif of ERK2[2], while the other inhibitors bind to the KIM site[3,4]. To estimate the origin of the difference in binding sites between the inhibitors, we performed a computer simulation analysis. Simulations were performed for each binding site of a single molecule of ERK2 in water, and their stable binding modes and binding free energies were calculated. A metadynamic simulation approach was used to predict the binding state from the dissociation state of the inhibitors without a priori assumption of the binding modes. The resulting binding modes to the KIM site and to the novel site showed different characteristics, reflecting the structural flexibility derived from the composition of the surrounding residues. Furthermore, the calculated binding free energies differed from the experimental results, with higher affinity on the KIM site than on the novel side. These results provide one hypothesis that the inhibitor interacts with a multichain binding site composed of ERK2 dimers, observed in crystal structure, rather than a single ERK2 binding site.
[1] T. Kinoshita, et al, Bioorg. & Med. Chem. Lett. 26: 955–958 (2016)
[2] M. Yoshida, et al, Biochem. Biophys. Res. Commun. 593: 73–78 (2022)
[3] H. Sugiyama, et al, Bioorg. & Med. Chem. Lett. 93: 129431 (2023)
[4] S. Hasegawa, et al, Biochem. Biophys. Res. Commun. 704: 149707 (2024)